Related papers: Development of a new force field for the family of…
Over the past decades, molecular dynamics (MD) simulations of biomolecules have become a mainstream biophysics technique. As the length and time scales amenable to the MD method increase, shortcomings of the empirical force fields---which…
Many commonly used force fields for protein systems such as AMBER, CHARMM, GROMACS, OPLS, and ECEPP have amino-acid-independent force-field parameters of main-chain torsion-energy terms. Here, we propose a new type of amino-acid-dependent…
We propose a novel method for refining force-field parameters of protein systems. In this method, the agreement of the secondary-structure stability and instability between the protein conformations obtained by experiments and those…
We demonstrate an automatic method of force field development for molecular simulations. Parameter tuning is taken as an optimization problem in many dimensions. The parameters are automatically adapted to reproduce known experimental data…
Traditional force fields commonly use a combination of bonded torsional terms and empirically scaled non-bonded interactions to capture 1-4 energies and forces of atoms separated by three bonds in a molecule. While this approach can yield…
Gaussian process (GP) emulator has been used as a surrogate model for predicting force field and molecular potential, to overcome the computational bottleneck of molecular dynamics simulation. Integrating both atomic force and energy in…
The solid acids CsH$_2$PO$_4$ and Cs$_7$(H$_4$PO$_4$)(H$_2$PO$_4$)$_8$ pose significant challenges for the simulation of proton transport phenomena. In this work, we use the recently developed machine-learned force field (MLFF) MACE to…
Numerous cell types relate to their immediate environment by exerting a three-dimensional pressure field on their environment, with components both longitudinal and transverse to the cell membrane. This pressure field can in principle be…
Classical molecular dynamics (MD) simulations enable modeling of materials and examination of microscopic details that are not accessible experimentally. The predictive capability of MD relies on the force field (FF) used to describe…
We propose a novel method to optimize existing force-field parameters for protein systems. The method consists of minimizing the summation of the square of the force acting on each atom in the proteins with the structures from the Protein…
Intrinsically disordered proteins (IDPs) play a significant role in intracellular phenomena and are known to exist in an ensemble of inter-converting conformations in solution. Accurately modeling the conformations of IDPs in solution poses…
Atomic partial charges appear in the Coulomb term of many force-field models and can be derived from electronic structure calculations with a myriad of atoms-in-molecules (AIM) methods. More advanced models have also been proposed, using…
In the context of nuclear fuel recycling and environmental issues, the understanding of the properties of radio-elements with various approaches remains a challenge regarding their dangerousness. Moreover, experimentally, it is imperative…
Molecular dynamics (MD) simulations allow atomistic insights into chemical and biological processes. Accurate MD simulations require computationally demanding quantum-mechanical calculations, being practically limited to short timescales…
Advancements in theoretical and algorithmic approaches, workflow engines, and an ever-increasing computational power have enabled a novel paradigm for materials discovery through first-principles high-throughput simulations. A major…
An atomic force microscope (AFM) is capable of producing ultra-high resolution measurements of nanoscopic objects and forces. It is an indispensable tool for various scientific disciplines such as molecular engineering, solid-state physics,…
A polarizable force-field (FF) model for short- and long-alkane chains and amide derivatives was constructed based solely on accurate quantum chemical (QC) calculations. First, the FF model accuracy was accessed by performing molecular…
The determination of potentials of mean force for solute insertion in a membrane by means of all-atom molecular dynamics simulations is often hampered by sampling issues. A multiscale approach to conformational sampling was recently…
Fast and accurate molecular force field (FF) parameterization is still an unsolved problem. Accurate FFs are not generally available for all molecules, like novel druglike molecules. While methods based on quantum mechanics (QM) exist to…
A novel embedded atom method (EAM) potential for the Xi-phases of Al-Pd-Mn has been determined with the force-matching method. Different combinations of analytic functions were tested for the pair and transfer part. The best results are…